Initial test of apex and oxford successful after refactoring includin…

…g with new definitions, next steps i) add eds, ii) testing and removing mismatch to appdef
FAIRmat-NFDI · Aug 30, 2024 · 8a98ea7 · 8a98ea7
1 parent cbab83e
commit 8a98ea7
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Showing 4 changed files with 15 additions and 13 deletions.
diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -38,8 +38,8 @@
                      //"../apex/InGaN_nanowires_linescan.edaxh5",
                      //"../apex/InGaN_nanowires_map.edaxh5",
                      //"../apex/InGaN_nanowires_spectra.edaxh5",
-                     "tests/data/2023-08-16_Ni_NFDI.edaxh5",
-                     //"tests/data/173_0057.h5oina",
+                     //"tests/data/2023-08-16_Ni_NFDI.edaxh5",
+                     "tests/data/173_0057.h5oina",
                      "--reader",
                      "em",
                      "--nxdl",
@@ -57,8 +57,8 @@
                      //"--output=pynxtools_em/dbg/zeiss.nxs",
                      //"--output=pynxtools_em/dbg/tfs.nxs",
                      //"--output=dbg/apex.nxs"
-                     //"--output=dbg/hfive_oxford.nxs",
-                     "--output=dbg/hfive_apex.nxs"],
+                     "--output=dbg/hfive_oxford.nxs",
+                     //"--output=dbg/hfive_apex.nxs"],
         }
     ]
 }
diff --git a/src/pynxtools_em/methods/ebsd.py b/src/pynxtools_em/methods/ebsd.py
@@ -222,10 +222,12 @@ def regrid_onto_equisized_scan_points(
     # TODO:: if scan_point_{dim} are calibrated this approach
     # here would shift the origin to 0, 0 implicitly which may not be desired
     if src_grid.dimensionality == 1:
-        tree = KDTree(np.column_stack((src_grid.pos["x"])))
+        tree = KDTree(np.column_stack((src_grid.pos["x"].magnitude)))
         d, idx = tree.query(trg_pos, k=1)
     elif src_grid.dimensionality == 2:
-        tree = KDTree(np.column_stack((src_grid.pos["x"], src_grid.pos["y"])))
+        tree = KDTree(
+            np.column_stack((src_grid.pos["x"].magnitude, src_grid.pos["y"].magnitude))
+        )
         d, idx = tree.query(trg_pos, k=1)
     if np.sum(idx == tree.n) > 0:
         raise ValueError(f"kdtree query left some query points without a neighbor!")

diff --git a/src/pynxtools_em/parsers/hfive_oxford.py b/src/pynxtools_em/parsers/hfive_oxford.py
@@ -234,12 +234,12 @@ def parse_and_normalize_slice_ebsd_phases(self, fp):
                 self.ebsd = EbsdPointCloud()
                 return
             latt = Lattice(
-                abc[0].magnitude,
-                abc[1].magnitude,
-                abc[2].magnitude,
-                angles[0].magnitude,
-                angles[1].magnitude,
-                angles[2].magnitude,
+                abc[0],
+                abc[1],
+                abc[2],
+                angles[0],
+                angles[1],
+                angles[2],
             )  # TODO:: lattice passed to kikuchipy I think needs to be in degree!
 
             # Space Group, no, H5T_NATIVE_INT32, (1, 1), Space group index.

diff --git a/src/pynxtools_em/utils/nx_default_plots.py b/src/pynxtools_em/utils/nx_default_plots.py
@@ -85,7 +85,7 @@ def priority_select(self, template: dict, entry_id: int = 1) -> dict:
                             break
 
             # find ebsd ipf map
-            idx_head = key.find("/ROI[roi1]")
+            idx_head = key.find("/roiID[roi1]")
             idx_tail = key.find("/ebsd/indexing")
             if idx_head is None or idx_tail is None:
                 continue